@khanacademy/perseus 19.1.5 → 19.1.6

package/src/widgets/molecule/smiles-parser.ts

@@ -1,296 +0,0 @@
-// Regexp defining characters that are valid SMILES characters that this parser
-// can parse.  In addition to serving as a sort of validation, this also keeps
-// out unimplemented features (like cycles and stereochemistry), which use
-// additional characters.
-const smilesRe = new RegExp("^[A-Za-z\\[\\]()=#+-]*$");
-
-// Regexp defining what characters are valid as atom names.  This includes
-// common 1-character elements, Cl and Br for convenience, and the open
-// bracket, which can be used to include anything as an atom name.
-const atomRe = new RegExp("^(Cl|Br|[CONPSFBI]|\\[)");
-
-function ParseError(message: string) {
-    // @ts-expect-error - TS2683 - 'this' implicitly has type 'any' because it does not have a type annotation.
-    this.message = message;
-}
-
-/**
- * Perform a functional update of a possibly nested object.
- *
- * Args:
- *     obj: an object, will not be modified
- *     keylist: a list of keys whose values will be updated in the object.
- *         This represents a path to a value inside nested objects.  For
- *         example, if keylist == ["a", "b", "c"], then a new object is
- *         returned with obj["a"]["b"]["c"] updated.  Note that if any of the
- *         keys is not already present, this will insert {} as a default value
- *         for that key.
- *     val: the new value to associate with the keypath
- *
- * Return: a new object, which is a shallow copy of the original with the value
- *     at the specified keypath replaced.
- */
-function _mset(obj, keylist, val) {
-    const k0 = keylist[0];
-    const rest = keylist.slice(1);
-    let newObj;
-    if (Array.isArray(obj)) {
-        newObj = [...obj];
-    } else {
-        newObj = {...(obj || {})};
-    }
-    let newVal = val;
-    if (rest.length > 0) {
-        newVal = _mset(newObj[k0], rest, val);
-    }
-    newObj[k0] = newVal;
-    return newObj;
-}
-
-/**
- * Perform a functional increment of a value in a nested object.
- *
- * Args:
- *     obj: an object; this will not be modified
- *     keylist: a list of keys representing a path into a nested object.  (See
- *         `_mset` for examples.)
- *
- * Return:
- *     an object that is a shallow copy of obj, with the value at the specified
- *     path incremeneted.
- */
-function _inc(obj, keylist: Array<number | string>) {
-    const val = keylist.reduce(function (acc, elt) {
-        return acc[elt];
-    }, obj);
-
-    return _mset(obj, keylist, val + 1);
-}
-
-function validate(smiles) {
-    return smilesRe.test(smiles);
-}
-
-/**
- * Parse a bond modifier character, updating the context object so that the
- * next bond created has this modifier.
- */
-function parseBondModifier(smiles: any, ctx) {
-    const firstChar = smiles[0];
-    const rest = smiles.slice(1);
-    if (firstChar === "=") {
-        return parse(rest, _mset(ctx, ["bond", "bondType"], "double"));
-    }
-    if (firstChar === "#") {
-        return parse(rest, _mset(ctx, ["bond", "bondType"], "triple"));
-    }
-    throw new ParseError("Invalid character: " + firstChar);
-}
-
-/**
- * Slice the input string, removing a parenthesized expression.
- * (Will handle nested parentheses.)
- *
- * parenStack should be a list containing any open parentheses already
- * encountered.  (Usually, this will be ["("])
- */
-function sliceFromMatchingCloseParen(smiles: any, parenStack: Array<any>) {
-    if (parenStack.length === 0) {
-        return smiles;
-    }
-
-    if (smiles === "") {
-        throw new ParseError("Mismatched parentheses");
-    }
-
-    const firstChar = smiles[0];
-    const rest = smiles.slice(1);
-
-    if (firstChar === "(") {
-        return sliceFromMatchingCloseParen(rest, parenStack.concat(firstChar));
-    }
-
-    if (firstChar === ")") {
-        return sliceFromMatchingCloseParen(rest, parenStack.slice(1));
-    }
-
-    return sliceFromMatchingCloseParen(rest, parenStack);
-}
-
-/**
- * Parse a branch, as indicated by the presence of a parenthesized experession.
- *
- * This returns a list of all branches (including the continuation of the
- * backbone) that should be added to the previous atom's bond list.
- */
-function parseParenthesizedExpression(smiles: any, ctx: any) {
-    const firstChar = smiles[0];
-    const rest = smiles.slice(1);
-    if (firstChar === "(") {
-        let newCtx = {...ctx, parens: ctx.parens + "("};
-        // increment the branch index
-        newCtx = _inc(ctx, ["idx", ctx.idx.length - 1, 1]);
-
-        let inBranchIdx = -1;
-        if (ctx.idx[ctx.idx.length - 1][0] % 2 === 0) {
-            // HACK(colin): this is so that we preserve the odd/even series in
-            // indices in branches; the layout engine uses this to select
-            // angles, and if we don't do this, editing one part of a molecule
-            // can cause another to flop around oddly.
-            // TODO(colin): this should just start at 0 all the time, and the
-            // layout engine should figure out continuity.
-            inBranchIdx = 0;
-        }
-        const parenCtx = {
-            ...newCtx,
-            idx: newCtx.idx.concat([[inBranchIdx, 0]]),
-            parens: newCtx.parens.concat("("),
-        } as const;
-        const parenExpr = parse(rest, parenCtx);
-        const remainder = parse(
-            sliceFromMatchingCloseParen(rest, ["("]),
-            newCtx,
-        );
-        return [parenExpr].concat(remainder);
-    }
-    if (firstChar === ")") {
-        if (ctx.parens[ctx.parens.length - 1] !== "(") {
-            throw new ParseError("Mismatched parentheses");
-        }
-        return null;
-    }
-    throw new ParseError("Invalid bare character: " + firstChar);
-}
-
-/**
- * Get the symbol of the next atom in the molecule.
- *
- * Return a 2-element list containing that symbol and the remainder of the
- * molecule.
- */
-function readAtomSymbol(smiles: any, _ctx) {
-    let sym = null;
-    let rest = null;
-    if (smiles[0] === "[") {
-        const closingIdx = smiles.indexOf("]");
-        if (closingIdx === -1) {
-            return ["", smiles];
-        }
-        sym = smiles.slice(1, closingIdx);
-        rest = smiles.slice(closingIdx + 1);
-    } else {
-        const match = atomRe.exec(smiles);
-        // @ts-expect-error - TS2322 - Type 'string' is not assignable to type 'null'. | TS2531 - Object is possibly 'null'.
-        sym = match[1];
-        // @ts-expect-error - TS2531 - Object is possibly 'null'.
-        rest = smiles.slice(sym.length);
-    }
-
-    return [sym, rest];
-}
-
-/**
- * Parse the next atom in the molecule, returning an atom object if this is the
- * first atom in the molecule, or a bond object with this atom as the
- * destination of the bond if this is not the first atom.
- */
-function parseAtom(smiles, ctx) {
-    const symbolInfo = readAtomSymbol(smiles, ctx);
-    const atom = symbolInfo[0];
-    if (atom === "") {
-        return ["error", "Unable to parse bracketed atom."];
-    }
-    const rest = symbolInfo[1];
-
-    // Atoms are indexed by a list of two-element lists.  In each two-element
-    // list, the first element is the atom counter, and the second element is
-    // the branch counter.  Branches are 1-indexed so that the main chain of
-    // the molecule can be indicated by 0.  Atoms may be either 0- or
-    // 1-indexed, defaulting to 1, to maintain a alternating pattern of
-    // odd/even indices. So, for example, if an atom has a branch off the main
-    // chain, and its atom index is x, then the indices of atoms are:
-    //     Atom where branch occurs: [[x, 0]]
-    //     First atom in the branch: [[x, 1], [1, 0]]  (assuming x is even)
-    //     Next atom in the main chain: [[x + 1, 0]]
-
-    // increment the atom counter and reset the branch counter
-    const newCtx = _mset(
-        ctx,
-        ["idx", ctx.idx.length - 1],
-        [1 + ctx.idx[ctx.idx.length - 1][0], 0],
-    );
-    let restOfMolecule = parse(
-        rest,
-        _mset(newCtx, ["bond", "bondType"], "single"),
-    );
-    if (!Array.isArray(restOfMolecule) && !!restOfMolecule) {
-        //TODO(colin): fix this awkwardness.
-        restOfMolecule = [restOfMolecule];
-    }
-    const atomObj = {
-        type: "atom",
-        symbol: atom,
-        bonds: restOfMolecule,
-        idx: newCtx.idx,
-    } as const;
-    if (ctx.bond) {
-        return {
-            type: "bond",
-            bondType: ctx.bond.bondType,
-            to: atomObj,
-        };
-    }
-    return atomObj;
-}
-
-function startsWithAtom(s: any) {
-    return atomRe.test(s);
-}
-
-function isModifierChar(s: any) {
-    return s === "=" || s === "#";
-}
-
-/**
- * Parse a SMILES string to an internal tree representation.
- *
- * Args:
- *   smiles [string]: a string representing the molecule.
- *
- * Returns: the parse tree (see top-of file docstring for details).
- *
- * Throws:
- *     ParseError: if the input is not valid SMILES or contains features not
- *         yet implemented.
- */
-function parse(smiles: any, ctx: any): any {
-    if (!validate(smiles)) {
-        throw new ParseError("Invalid input.");
-    }
-
-    if (!smiles || smiles.length === 0) {
-        return null;
-    }
-
-    if (startsWithAtom(smiles)) {
-        return parseAtom(
-            smiles,
-            ctx || {
-                idx: [[0, 0]],
-                parens: [],
-                stack: [],
-                bondModifiers: [],
-            },
-        );
-    }
-    if (isModifierChar(smiles[0])) {
-        // TODO(colin): add a better error message in the case where the input
-        // is invalid and starts with a modifier character?
-        return parseBondModifier(smiles, ctx);
-    }
-    // TODO(colin): add additional cases for unimplemented bits of SMILES
-    // syntax.
-    return parseParenthesizedExpression(smiles, ctx);
-}
-
-export default {parse: parse, ParseError: ParseError};

package/src/widgets/molecule.tsx

@@ -1,172 +0,0 @@
-/* eslint-disable react/no-unsafe */
-import * as i18n from "@khanacademy/wonder-blocks-i18n";
-import PropTypes from "prop-types";
-import * as React from "react";
-
-import draw from "./molecule/molecule-drawing";
-import MoleculeLayout from "./molecule/molecule-layout";
-import SmilesParser from "./molecule/smiles-parser";
-
-import type {WidgetExports} from "../types";
-
-const {layout} = MoleculeLayout;
-const parse = SmilesParser.parse;
-const ParseError = SmilesParser.ParseError;
-
-const borderSize = 30;
-
-export class Molecule extends React.Component<any, any> {
-    static propTypes = {
-        id: PropTypes.string.isRequired,
-        rotationAngle: PropTypes.number,
-        smiles: PropTypes.string,
-    };
-
-    state: any = {parsedSmiles: null, error: null};
-
-    // TODO(jangmi, CP-3288): Remove usage of `UNSAFE_componentWillMount`
-    UNSAFE_componentWillMount() {
-        this.stateFromSmiles(this.props.smiles);
-    }
-
-    componentDidMount() {
-        this.canvasRender();
-    }
-
-    UNSAFE_componentWillReceiveProps(nextProps: any) {
-        this.stateFromSmiles(nextProps.smiles);
-    }
-
-    componentDidUpdate() {
-        this.canvasRender();
-    }
-
-    stateFromSmiles: (arg1: any) => void = (smiles) => {
-        try {
-            this.setState({
-                // @ts-expect-error - TS2554 - Expected 2 arguments, but got 1.
-                parsedSmiles: parse(smiles),
-                error: null,
-            });
-        } catch (e: any) {
-            if (e instanceof ParseError) {
-                // @ts-expect-error - TS2339 - Property 'message' does not exist on type '{}'.
-                this.setState({error: e.message});
-            } else {
-                throw e;
-            }
-        }
-    };
-
-    setCanvasBounds: (arg1: any, arg2: any) => any = (canvas, items) => {
-        const xmax = Math.max(
-            ...items.map((item) => (item.pos ? item.pos[0] : -Infinity)),
-        );
-        const ymax = Math.max(
-            ...items.map((item) => (item.pos ? item.pos[1] : -Infinity)),
-        );
-        const xmin = Math.min(
-            ...items.map((item) => (item.pos ? item.pos[0] : Infinity)),
-        );
-        const ymin = Math.min(
-            ...items.map((item) => (item.pos ? item.pos[1] : Infinity)),
-        );
-        const width = xmax - xmin + 2 * borderSize;
-        const height = ymax - ymin + 2 * borderSize;
-        canvas.width = width;
-        canvas.height = height;
-        return [borderSize - xmin, borderSize - ymin];
-    };
-
-    canvasRender: () => void = () => {
-        // Since canvas drawing happens only through an imperative API, we sync
-        // up the component with the canvas here, which happens when the
-        // component mounts or updates.
-        if (!!this.state.error || !this.state.parsedSmiles) {
-            return;
-        }
-        const items = layout(this.state.parsedSmiles, this.props.rotationAngle);
-        // eslint-disable-next-line react/no-string-refs
-        const canvas = this.refs.canvas;
-        const translation = this.setCanvasBounds(canvas, items);
-        // @ts-expect-error - TS2339 - Property 'getContext' does not exist on type 'ReactInstance'.
-        const ctx = canvas.getContext("2d");
-        // @ts-expect-error - TS2339 - Property 'width' does not exist on type 'ReactInstance'. | TS2339 - Property 'height' does not exist on type 'ReactInstance'.
-        ctx.clearRect(0, 0, canvas.width, canvas.height);
-        ctx.save();
-        ctx.translate(translation[0], translation[1]);
-        draw(ctx, items);
-        ctx.restore();
-    };
-
-    render(): React.ReactNode {
-        // TODO(colin): escape the punctuation in the SMILES alt text for
-        // screen readers?
-        let content = (
-            <canvas
-                className="molecule-canvas"
-                id={this.props.id + "-molecule"}
-                // eslint-disable-next-line react/no-string-refs
-                ref="canvas"
-            >
-                {i18n.$_(
-                    "A molecular structure drawing. SMILES notation: %(content)s",
-                    {
-                        content: this.props.smiles,
-                    },
-                )}
-            </canvas>
-        );
-        if (this.state.error) {
-            content = <div className="error">{this.state.error}</div>;
-        }
-        return <div className="molecule-canvas">{content}</div>;
-    }
-}
-
-class MoleculeWidget extends React.Component<any> {
-    static propTypes = {
-        rotationAngle: PropTypes.number,
-        smiles: PropTypes.string,
-        widgetId: PropTypes.string,
-    };
-
-    static defaultProps: any = {rotationAngle: 0};
-
-    simpleValidate: (arg1: any) => any = () => {
-        return {type: "points", earned: 0, total: 0, message: null};
-    };
-
-    getUserInput: () => ReadonlyArray<ReadonlyArray<string>> = () => {
-        return [];
-    };
-
-    validate: (arg1: any, arg2: any) => any = (state, rubric) => {
-        // TODO(colin): this is here as part of the interface for a component.
-        // Figure out if there is something more appropriate that this should
-        // return.
-        return {
-            type: "points",
-            earned: 0,
-            total: 0,
-            message: null,
-        };
-    };
-
-    render(): React.ReactNode {
-        return (
-            <Molecule
-                id={this.props.widgetId}
-                smiles={this.props.smiles}
-                rotationAngle={this.props.rotationAngle}
-            />
-        );
-    }
-}
-
-export default {
-    name: "molecule-renderer",
-    displayName: "Molecule renderer",
-    hidden: true,
-    widget: MoleculeWidget,
-} as WidgetExports<typeof MoleculeWidget>;